People

Sophie Abby received a bi-disciplinary education in biology and computer sciences. She is an evolutionary biologist, particularly interested in the mechanisms of diversification of archaea and bacteria. She studies these at different scales: from enzymes and metabolic pathways, to macromolecular complexes and genome dynamics in response to environmental adaptations. She also develops methods in the field of comparative genomics and phylogenomics, in particular for genome annotation.

Ivan Junier is the resident biophysicist expert. He works on rationalising the tinkering that has shaped the content, organisation and structuring of bacterial genomes. To this end, he develops quantitative, biophysical models of DNA in interaction with various fundamental proteins and molecular machineries that are crucial for gene expression, chromosome replication and chromosome segregation. To navigate in the (sometimes dark) space of bacterial genomes, he uses comparative genomics and statistical methods to distinguish between universal and idiosyncratic features.

Nelle Varoquaux is a machine.

Victor Bañon Garcia is a PHD student working on “Systematic study of inverted repeated sequences in prokaryotic genomes” under the supervision of Ivan Junier and Nelle Varoquaux.

Emma Bouvet is a PhD student supervised by Sophie Abby and Ludovic Pelosi. She works on the evolution of quinone biosynthetic pathways in bacteria and eukaryotes.

Flora Gaudillière is an assistant professor working on the evolutionary dynamics of insertion sequences, a type of autonomous mobile DNA sequences found in most prokaryotic genomes. She combines bioinformatic approaches with wet lab experiments. She is interested in genome ecology: can we apply concepts and tools developed in the field of ecology to understand the dynamics of mobile genetic elements, understood as individuals populating a genomic ecosystem?

Sandy Frank Kwamou Ngaha is a PhD student working on the Detection of new secretion systems in collaboration with experts in these systems under the supervisions of Nelle VAROQUAUX and Sophie ABBY

Gabin Laurent is a postdoctoral researcher working on the physical modeling of DNA transcription and replication in bacteria.

Alexis Nguyen is an engineer supervised by Sophie Abby and Fabien Pierrel. He works on the ADAPT2Q project about the adjustment of bioenergetic enzymes to quinones.

Morgane Roger-Margueritat is a PhD student working on the impact of quinone exchanges on the gut microbiota. She combines experimental and bioinformatic approaches. She is supervised by Fabien Pierrel and Sophie Abby.

Timothee Salzat-Hervouette is a PhD student working to understand the evolution and taxonomic distribution of phototrophy in Pseudomonadota. He is supervised by Sophie Abby and Fabien Pierrel.

Zakaria Tougui is a PhD student working on the quantitative characterisation of the human gut microbiome, with a focus on the small intestine, combining publicly available data with data obtained from collaborators at TIMC using a newly developped non-invasive sampling method. This thesis is supervised by Antoine Frénoy, Nelle Varoquaux and Philippe Cinquin